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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs199549612

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:154571768 (GRCh38.p14) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000015 (4/264690, TOPMED)
T=0.000021 (3/140314, GnomAD)
T=0.00006 (2/35412, ALFA) (+ 1 more)
T=0.00008 (1/13006, GO-ESP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CHRNB2 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 51772 C=0.99996 T=0.00004
European Sub 36660 C=0.99997 T=0.00003
African Sub 7756 C=1.0000 T=0.0000
African Others Sub 298 C=1.000 T=0.000
African American Sub 7458 C=1.0000 T=0.0000
Asian Sub 112 C=1.000 T=0.000
East Asian Sub 86 C=1.00 T=0.00
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 498 C=1.000 T=0.000
Latin American 2 Sub 628 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 6020 C=0.9998 T=0.0002


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 C=0.999985 T=0.000015
gnomAD - Genomes Global Study-wide 140314 C=0.999979 T=0.000021
gnomAD - Genomes European Sub 75966 C=0.99997 T=0.00003
gnomAD - Genomes African Sub 42068 C=0.99998 T=0.00002
gnomAD - Genomes American Sub 13670 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2152 C=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 35412 C=0.99994 T=0.00006
Allele Frequency Aggregator European Sub 26572 C=0.99996 T=0.00004
Allele Frequency Aggregator Other Sub 4586 C=0.9998 T=0.0002
Allele Frequency Aggregator African Sub 2918 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 498 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
GO Exome Sequencing Project Global Study-wide 13006 C=0.99992 T=0.00008
GO Exome Sequencing Project European American Sub 8600 C=1.0000 T=0.0000
GO Exome Sequencing Project African American Sub 4406 C=0.9998 T=0.0002
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p14 chr 1 NC_000001.11:g.154571768C>G
GRCh38.p14 chr 1 NC_000001.11:g.154571768C>T
GRCh37.p13 chr 1 NC_000001.10:g.154544244C>G
GRCh37.p13 chr 1 NC_000001.10:g.154544244C>T
CHRNB2 RefSeqGene NG_008027.1:g.8988C>G
CHRNB2 RefSeqGene NG_008027.1:g.8988C>T
Gene: CHRNB2, cholinergic receptor nicotinic beta 2 subunit (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CHRNB2 transcript NM_000748.3:c.945C>G S [AGC] > R [AGG] Coding Sequence Variant
neuronal acetylcholine receptor subunit beta-2 precursor NP_000739.1:p.Ser315Arg S (Ser) > R (Arg) Missense Variant
CHRNB2 transcript NM_000748.3:c.945C>T S [AGC] > S [AGT] Coding Sequence Variant
neuronal acetylcholine receptor subunit beta-2 precursor NP_000739.1:p.Ser315= S (Ser) > S (Ser) Synonymous Variant
CHRNB2 transcript variant X2 XM_017000180.3:c.435C>G S [AGC] > R [AGG] Coding Sequence Variant
neuronal acetylcholine receptor subunit beta-2 isoform X1 XP_016855669.1:p.Ser145Arg S (Ser) > R (Arg) Missense Variant
CHRNB2 transcript variant X2 XM_017000180.3:c.435C>T S [AGC] > S [AGT] Coding Sequence Variant
neuronal acetylcholine receptor subunit beta-2 isoform X1 XP_016855669.1:p.Ser145= S (Ser) > S (Ser) Synonymous Variant
CHRNB2 transcript variant X1 XR_001736952.3:n.1212C>G N/A Non Coding Transcript Variant
CHRNB2 transcript variant X1 XR_001736952.3:n.1212C>T N/A Non Coding Transcript Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: T (allele ID: 941469 )
ClinVar Accession Disease Names Clinical Significance
RCV001232809.5 Autosomal dominant nocturnal frontal lobe epilepsy Uncertain-Significance
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement C= G T
GRCh38.p14 chr 1 NC_000001.11:g.154571768= NC_000001.11:g.154571768C>G NC_000001.11:g.154571768C>T
GRCh37.p13 chr 1 NC_000001.10:g.154544244= NC_000001.10:g.154544244C>G NC_000001.10:g.154544244C>T
CHRNB2 RefSeqGene NG_008027.1:g.8988= NG_008027.1:g.8988C>G NG_008027.1:g.8988C>T
CHRNB2 transcript NM_000748.3:c.945= NM_000748.3:c.945C>G NM_000748.3:c.945C>T
CHRNB2 transcript NM_000748.2:c.945= NM_000748.2:c.945C>G NM_000748.2:c.945C>T
CHRNB2 transcript variant X2 XM_017000180.3:c.435= XM_017000180.3:c.435C>G XM_017000180.3:c.435C>T
CHRNB2 transcript variant X2 XM_017000180.2:c.435= XM_017000180.2:c.435C>G XM_017000180.2:c.435C>T
CHRNB2 transcript variant X2 XM_017000180.1:c.435= XM_017000180.1:c.435C>G XM_017000180.1:c.435C>T
CHRNB2 transcript variant X1 XR_001736952.3:n.1212= XR_001736952.3:n.1212C>G XR_001736952.3:n.1212C>T
CHRNB2 transcript variant X1 XR_001736952.2:n.1197= XR_001736952.2:n.1197C>G XR_001736952.2:n.1197C>T
CHRNB2 transcript variant X1 XR_001736952.1:n.1197= XR_001736952.1:n.1197C>G XR_001736952.1:n.1197C>T
neuronal acetylcholine receptor subunit beta-2 precursor NP_000739.1:p.Ser315= NP_000739.1:p.Ser315Arg NP_000739.1:p.Ser315=
neuronal acetylcholine receptor subunit beta-2 isoform X1 XP_016855669.1:p.Ser145= XP_016855669.1:p.Ser145Arg XP_016855669.1:p.Ser145=
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

6 SubSNP, 6 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 GSK-GENETICS ss491235480 May 04, 2012 (137)
2 NHLBI-ESP ss712346835 Apr 25, 2013 (138)
3 GNOMAD ss2731893123 Nov 08, 2017 (151)
4 EVA ss3823663157 Apr 25, 2020 (154)
5 GNOMAD ss4003733950 Apr 25, 2021 (155)
6 TOPMED ss4468300105 Apr 25, 2021 (155)
7 gnomAD - Genomes NC_000001.11 - 154571768 Apr 25, 2021 (155)
8 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 915532 (NC_000001.10:154544243:C:C 251067/251068, NC_000001.10:154544243:C:G 1/251068)
Row 915533 (NC_000001.10:154544243:C:C 251067/251068, NC_000001.10:154544243:C:T 1/251068)

- Jul 12, 2019 (153)
9 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 915532 (NC_000001.10:154544243:C:C 251067/251068, NC_000001.10:154544243:C:G 1/251068)
Row 915533 (NC_000001.10:154544243:C:C 251067/251068, NC_000001.10:154544243:C:T 1/251068)

- Jul 12, 2019 (153)
10 GO Exome Sequencing Project NC_000001.10 - 154544244 Oct 11, 2018 (152)
11 TopMed NC_000001.11 - 154571768 Apr 25, 2021 (155)
12 ALFA NC_000001.11 - 154571768 Apr 25, 2021 (155)
13 ClinVar RCV001232809.5 Oct 12, 2022 (156)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2731893123 NC_000001.10:154544243:C:G NC_000001.11:154571767:C:G (self)
ss491235480 NC_000001.9:152810867:C:T NC_000001.11:154571767:C:T (self)
121755, ss712346835, ss2731893123, ss3823663157 NC_000001.10:154544243:C:T NC_000001.11:154571767:C:T (self)
RCV001232809.5, 27049512, 31906440, 9463797352, ss4003733950, ss4468300105 NC_000001.11:154571767:C:T NC_000001.11:154571767:C:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs199549612

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post761+d5e8e07